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''Paenarthrobacter ureafaciens'' KI72, popularly known as nylon-eating bacteria, is a strain of '' Paenarthrobacter ureafaciens'' that can digest certain
by-product A by-product or byproduct is a secondary product derived from a production process, manufacturing process or chemical reaction; it is not the primary product or service being produced. A by-product can be useful and marketable or it can be consid ...
s of
nylon 6 Nylon 6 or polycaprolactam is a polymer, in particular semicrystalline polyamide. Unlike most other nylons, nylon 6 is not a condensation polymer, but instead is formed by ring-opening polymerization; this makes it a special case in the compari ...
manufacture. It uses a set of
enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. ...
s to digest nylon, popularly known as nylonase.


Discovery and nomenclature

In 1975, a team of Japanese scientists discovered a strain of bacterium, living in ponds containing
waste water Wastewater is water generated after the use of freshwater, raw water, drinking water or saline water in a variety of deliberate applications or processes. Another definition of wastewater is "Used water from any combination of domestic, industrial ...
from a
nylon Nylon is a generic designation for a family of synthetic polymers composed of polyamides ( repeating units linked by amide links).The polyamides may be aliphatic or semi-aromatic. Nylon is a silk-like thermoplastic, generally made from petr ...
factory, that could digest certain byproducts of
nylon 6 Nylon 6 or polycaprolactam is a polymer, in particular semicrystalline polyamide. Unlike most other nylons, nylon 6 is not a condensation polymer, but instead is formed by ring-opening polymerization; this makes it a special case in the compari ...
manufacture, such as the linear dimer of 6-aminohexanoate. These substances are not known to have existed before the invention of
nylon Nylon is a generic designation for a family of synthetic polymers composed of polyamides ( repeating units linked by amide links).The polyamides may be aliphatic or semi-aromatic. Nylon is a silk-like thermoplastic, generally made from petr ...
in 1935. It was initially named as '' Achromobacter guttatus''. Studies in 1977 revealed that the three
enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. ...
s that the bacteria were using to digest the byproducts were significantly different from any other enzymes produced by any other bacteria, and not effective on any material other than the manmade nylon byproducts. The bacterium was reassigned to ''
Flavobacterium ''Flavobacterium'' is a genus of Gram-negative, nonmotile and motile, rod-shaped bacteria that consists of 130 recognized species. Flavobacteria are found in soil and fresh water in a variety of environments. Several species are known to cause ...
'' in 1980. Its genome was resolved in 2017, again reassigning it to ''
Arthrobacter ''Arthrobacter'' (from the Greek, "jointed small stick”) is a genus of bacteria that is commonly found in soil. All species in this genus are Gram-positive obligate aerobes that are rods during exponential growth and cocci in their stationar ...
''. The
Genome Taxonomy Database The Genome Taxonomy Database (GTDB) is an online database that maintains information on a proposed nomenclature of prokaryotes, following a phylogenomic approach based on a set of conserved single-copy proteins. In addition to breaking up paraphy ...
considers it a strain of '' Paenarthrobacter ureafaciens'' following a 2016 reclassification. As of January 2021, the NCBI taxonomy browser has been updated to match GTDB.


Descendent strains

A few newer strains have been created by growing the original KI72 in different conditions, forcing it to adapt. These include KI722, KI723, KI723T1, KI725, KI725R, and many more.


The enzymes

The bacterium contains the following three enzymes: * 6-aminohexanoate-cyclic-dimer hydrolase (EI, ''NylA'', ) * 6-aminohexanoate-dimer hydrolase (EII, ''NylB'', ) * 6-aminohexanoate-oligomer endohydrolase (EIII, ''NylC'', ) All three enzymes are encoded on a
plasmid A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; ho ...
called pOAD2. The plasmid can be transferred to ''
E. coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Es ...
'', as shown in a 1983 publication.


EI

The enzyme EI is related to
amidase In enzymology, an amidase (, ''acylamidase'', ''acylase (misleading)'', ''amidohydrolase (ambiguous)'', ''deaminase (ambiguous)'', ''fatty acylamidase'', ''N-acetylaminohydrolase (ambiguous)'') is an enzyme that catalyzes the hydrolysis of an ami ...
s. Its structure was resolved in 2010.


EII

EII has evolved by gene duplication followed by base substitution of another protein EII'. Both enzymes have 345 identical aminoacids out of 392 aminoacids (88% homology). The enzymes are similar to
beta-lactamase Beta-lactamases, (β-lactamases) are enzymes () produced by bacteria that provide multi-resistance to beta-lactam antibiotics such as penicillins, cephalosporins, cephamycins, monobactams and carbapenems ( ertapenem), although carbapene ...
. The EII' (''NylB, ) protein is about 100x times less efficient compared to EII. A 2007 research by the Seiji Negoro team shows that just two amino-acid alterations to EII', i.e. G181D and H266N, raises its activity to 85% of EII.


EIII

The structure of EIII was resolved in 2018. Instead of being a completely novel enzyme, it appears to be a member of the N-terminal nucleophile (N-tn) hydrolase family. Specifically, computational approaches classify it as a
MEROPS MEROPS is an online database for peptidases (also known as proteases, proteinases and proteolytic enzymes) and their inhibitors. The classification scheme for peptidases was published by Rawlings & Barrett in 1993, and that for protein inhibitor ...
S58 (now renamed P1) hydrolase. The protein is expressed as a precursor, which then cleaves itself into two chains. Outside of this plasmid, > 95% similar proteins are found in '' Agromyces'' and '' Kocuria''. EIII was originally thought to be completely novel.
Susumu Ohno Susumu is a masculine Japanese given name. Notable people with the name include: * Susumu Akagi (born 1972) Japanese voice actor * Susumu Aoyagi (青柳 進, born 1968), Japanese baseball player * Susumu Chiba (born 1970), Japanese voice actor *, ...
proposed that it had come about from the combination of a gene-duplication event with a
frameshift mutation A frameshift mutation (also called a framing error or a reading frame shift) is a genetic mutation caused by indels ( insertions or deletions) of a number of nucleotides in a DNA sequence that is not divisible by three. Due to the triplet nature ...
. An insertion of
thymidine Thymidine (symbol dT or dThd), also known as deoxythymidine, deoxyribosylthymine, or thymine deoxyriboside, is a pyrimidine deoxynucleoside. Deoxythymidine is the DNA nucleoside T, which pairs with deoxyadenosine (A) in double-stranded DNA. ...
would turn an arginine-rich 427aa protein into this 392aa enzyme.


Role in evolution teaching

There is scientific consensus that the capacity to synthesize nylonase most probably developed as a single-step mutation that survived because it improved the fitness of the bacteria possessing the mutation. More importantly, the enzyme involved was produced by a mutation completely randomizing the original gene. Despite this, the new gene still had a novel, albeit weak, catalytic capacity. This is seen as a good example of how mutations easily can provide the raw material for
evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
by
natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Charl ...
. A 1995 paper showed that scientists have also been able to induce another species of bacterium, ''
Pseudomonas aeruginosa ''Pseudomonas aeruginosa'' is a common encapsulated, gram-negative, aerobic– facultatively anaerobic, rod-shaped bacterium that can cause disease in plants and animals, including humans. A species of considerable medical importance, ''P. aeru ...
'', to evolve the capability to break down the same nylon byproducts in a laboratory by forcing them to live in an environment with no other source of nutrients. The ''P. aeruginosa'' strain NK87 did not seem to use the same enzymes that had been utilized by the original KI72 strain.


See also

* Organisms breaking down plastic *
Biodegradable plastic Biodegradable plastics are plastics that can be decomposed by the action of living organisms, usually microbes, into water, carbon dioxide, and biomass. Biodegradable plastics are commonly produced with renewable raw materials, micro-organisms, ...
* ''E. coli'' long-term evolution experiment *
Radiotrophic fungus Radiotrophic fungi are fungi that can use radiation as an energy source to stimulate growth. Radiotrophic fungi have been found in extreme environments such as in the Chernobyl Nuclear Power Plant. Most known radiotrophic fungi utilize melanin i ...
* London Underground mosquito * ''Lonicera'' fly *
Mealworm Mealworms are the larval form of the yellow mealworm beetle, ''Tenebrio molitor'', a species of darkling beetle. Like all holometabolic insects, they go through four life stages: egg, larva, pupa, and adult. Larvae typically measure about ...
s are capable of digesting
polystyrene Polystyrene (PS) is a synthetic polymer made from monomers of the aromatic hydrocarbon styrene. Polystyrene can be solid or foamed. General-purpose polystyrene is clear, hard, and brittle. It is an inexpensive resin per unit weight. It is a ...


References

*


External links


NBRC 14590
information on the KI72 culture maintained at
National Institute of Technology and Evaluation The , or NITE is an Independent Administrative Institution, established by Japanese government, aiming to contribute to the "safety and security of life" supported by reliable technology and information. History The predecessors of NITE were f ...
*
NBRC 114184
a derived culture used in the 2017 sequencing * {{Authority control Biological evolution Organisms breaking down plastic Actinomycetota